def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
template = ForceField._TemplateData(template_name)
for atom in residue.atoms():
typename = 'XXX'
atom_template = ForceField._TemplateAtomData(atom.name, typename, atom.element)
template.atoms.append(atom_template)
for (atom1,atom2) in residue.internal_bonds():
template.addBondByName(atom1.name, atom2.name)
residue_atoms = [ atom for atom in residue.atoms() ]
for (atom1,atom2) in residue.external_bonds():
if atom1 in residue_atoms:
template.addExternalBondByName(atom1.name)
elif atom2 in residue_atoms:
template.addExternalBondByName(atom2.name)
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
template = ForceField._TemplateData(template_name)
for atom in residue.atoms():
typename = "XXX"
atom_template = ForceField._TemplateAtomData(atom.name, typename, atom.element)
template.atoms.append(atom_template)
for (atom1, atom2) in residue.internal_bonds():
template.addBondByName(atom1.name, atom2.name)
residue_atoms = [atom for atom in residue.atoms()]
for (atom1, atom2) in residue.external_bonds():
if atom1 in residue_atoms:
template.addExternalBondByName(atom1.name)
elif atom2 in residue_atoms:
template.addExternalBondByName(atom2.name)
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
from simtk.openmm.app.forcefield import _createResidueTemplate
template = _createResidueTemplate(residue) # use helper function
template.name = template_name # replace template name
for (template_atom, residue_atom) in zip(template.atoms, residue.atoms()):
template_atom.type = 'XXX' # replace atom type
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
from simtk.openmm.app.forcefield import _createResidueTemplate
template = _createResidueTemplate(residue) # use helper function
template.name = template_name # replace template name
for (template_atom, residue_atom) in zip(template.atoms, residue.atoms()):
template_atom.type = 'XXX' # replace atom type
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([ residue.name for residue in residues ])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([ template.name for template in templates ])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([residue.name for residue in residues])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([template.name for template in templates])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(
os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml',
StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=NoCutoff)
